Revision 10625
Added by Aaron Marcuse-Kubitza over 11 years ago
| inputs/TEX/Specimen/postprocess.sql | ||
|---|---|---|
| 2 | 2 |
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| 3 | 3 |
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| 4 | 4 |
SELECT mk_derived_col((:table_str, 'dateCollected'), |
| 5 |
$$_alt("COLL. DATE (EXACT)", "COLL. DATE (GENERAL)")$$)
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|
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$$_alt("dateCollected__scrubbed", "dateCollected__verbatim")$$)
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|
| 6 | 6 |
; -- runtime: 2 s ("Time: 1734.640 ms") @starscream
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| inputs/TEX/Specimen/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
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| 0 | 3 | |
| inputs/TEX/Specimen/map.csv | ||
|---|---|---|
| 36 | 36 |
DATA ENTRY BY,*DATA ENTRY BY,, |
| 37 | 37 |
DATA ENTRY DATE,*DATA ENTRY DATE,, |
| 38 | 38 |
DATA EDITED DATE,modified,, |
| 39 |
dateCollected,dateCollected,, |
|
| inputs/TEX/Specimen/test.xml.ref | ||
|---|---|---|
| 9 | 9 |
<location> |
| 10 | 10 |
<authorlocationcode> |
| 11 | 11 |
<_join> |
| 12 |
<2>$HERBARIUM</2>
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|
| 13 |
<3>$ACCESSION NO.</3>
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|
| 12 |
<2>$collection</2>
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|
| 13 |
<3>$accessionNumber</3>
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|
| 14 | 14 |
</_join> |
| 15 | 15 |
</authorlocationcode> |
| 16 | 16 |
<elevation_m> |
| 17 | 17 |
<_units> |
| 18 | 18 |
<to>m</to> |
| 19 | 19 |
<to></to> |
| 20 |
<value>$ELEVATION</value>
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|
| 20 |
<value>$verbatimElevation</value>
|
|
| 21 | 21 |
</_units> |
| 22 | 22 |
</elevation_m> |
| 23 | 23 |
<iscultivated> |
| 24 | 24 |
<_locationnarrative_is_cultivated> |
| 25 | 25 |
<locationnarrative> |
| 26 | 26 |
<_join> |
| 27 |
<1>$LOCATION</1>
|
|
| 28 |
<3>$ECOLOGICAL INFORMATION</3>
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|
| 27 |
<1>$locality</1>
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|
| 28 |
<3>$habitat</3>
|
|
| 29 | 29 |
</_join> |
| 30 | 30 |
</locationnarrative> |
| 31 | 31 |
</_locationnarrative_is_cultivated> |
| ... | ... | |
| 34 | 34 |
<taxonoccurrence> |
| 35 | 35 |
<aggregateoccurrence> |
| 36 | 36 |
<collectiondate>$dateCollected</collectiondate> |
| 37 |
<notes>$SPECIMEN NOTES</notes>
|
|
| 37 |
<notes>$occurrenceRemarks</notes>
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|
| 38 | 38 |
<plantobservation> |
| 39 |
<authorplantcode>$COLLECTOR NUMBER</authorplantcode>
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|
| 40 |
<reproductivecondition>$PHENOLOGY</reproductivecondition>
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|
| 39 |
<authorplantcode>$collectorNumber</authorplantcode>
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|
| 40 |
<reproductivecondition>$reproductiveCondition</reproductivecondition>
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|
| 41 | 41 |
<specimenreplicate> |
| 42 |
<catalognumber_dwc>$ACCESSION NO.</catalognumber_dwc>
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| 43 |
<collectioncode_dwc>$HERBARIUM</collectioncode_dwc>
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<collectionnumber>$COLLECTOR NUMBER</collectionnumber>
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|
| 42 |
<catalognumber_dwc>$accessionNumber</catalognumber_dwc>
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<collectioncode_dwc>$collection</collectioncode_dwc>
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| 44 |
<collectionnumber>$collectorNumber</collectionnumber>
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|
| 45 | 45 |
</specimenreplicate> |
| 46 | 46 |
</plantobservation> |
| 47 | 47 |
</aggregateoccurrence> |
| 48 |
<collector_id><party><fullname>$COLLECTOR NAME(S)</fullname></party></collector_id>
|
|
| 48 |
<collector_id><party><fullname>$recordedBy</fullname></party></collector_id>
|
|
| 49 | 49 |
<iscultivated> |
| 50 | 50 |
<_map> |
| 51 | 51 |
<cultivated>t</cultivated> |
| 52 | 52 |
<wild>f</wild> |
| 53 | 53 |
<*></*> |
| 54 |
<value>$ORIGIN</value>
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|
| 54 |
<value>$establishmentMeans</value>
|
|
| 55 | 55 |
</_map> |
| 56 | 56 |
</iscultivated> |
| 57 | 57 |
<isnative> |
| ... | ... | |
| 59 | 59 |
<native>t</native> |
| 60 | 60 |
<exotic>f</exotic> |
| 61 | 61 |
<*></*> |
| 62 |
<value>$ORIGIN</value>
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|
| 62 |
<value>$establishmentMeans</value>
|
|
| 63 | 63 |
</_map> |
| 64 | 64 |
</isnative> |
| 65 | 65 |
<taxondetermination> |
| 66 |
<party_id><party><fullname>$DETERMINED BY</fullname></party></party_id>
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|
| 66 |
<party_id><party><fullname>$identifiedBy</fullname></party></party_id>
|
|
| 67 | 67 |
<taxonverbatim_id> |
| 68 | 68 |
<taxonverbatim> |
| 69 | 69 |
<taxonlabel_id> |
| ... | ... | |
| 85 | 85 |
<parent_id> |
| 86 | 86 |
<taxonlabel> |
| 87 | 87 |
<rank>species</rank> |
| 88 |
<taxonepithet>$SPECIES</taxonepithet>
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|
| 88 |
<taxonepithet>$specificEpithet</taxonepithet>
|
|
| 89 | 89 |
<parent_id> |
| 90 | 90 |
<taxonlabel> |
| 91 | 91 |
<rank>genus</rank> |
| 92 |
<taxonepithet>$GENUS</taxonepithet>
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|
| 92 |
<taxonepithet>$genus</taxonepithet>
|
|
| 93 | 93 |
<parent_id> |
| 94 | 94 |
<taxonlabel> |
| 95 | 95 |
<rank>family</rank> |
| 96 |
<taxonepithet>$FAMILY</taxonepithet>
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|
| 96 |
<taxonepithet>$family</taxonepithet>
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|
| 97 | 97 |
</taxonlabel> |
| 98 | 98 |
</parent_id> |
| 99 | 99 |
</taxonlabel> |
| ... | ... | |
| 108 | 108 |
</parent_id> |
| 109 | 109 |
</taxonlabel> |
| 110 | 110 |
</parent_id> |
| 111 |
<taxonepithet>$INFRA NAME</taxonepithet>
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|
| 111 |
<taxonepithet>$infraspecificEpithet</taxonepithet>
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|
| 112 | 112 |
</taxonlabel> |
| 113 | 113 |
</parent_id> |
| 114 | 114 |
<taxonomicname> |
| 115 | 115 |
<_merge_prefix> |
| 116 |
<prefix><_taxon_family_require_std><family>$FAMILY</family></_taxon_family_require_std></prefix>
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|
| 116 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
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|
| 117 | 117 |
<value> |
| 118 | 118 |
<_join_words> |
| 119 | 119 |
<1> |
| 120 | 120 |
<_join_words> |
| 121 |
<2><_filter_genus><value>$GENUS</value></_filter_genus></2>
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|
| 122 |
<3>$SPECIES</3>
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| 123 |
<5>$INFRA NAME</5>
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|
| 121 |
<2><_filter_genus><value>$genus</value></_filter_genus></2>
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|
| 122 |
<3>$specificEpithet</3>
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|
| 123 |
<5>$infraspecificEpithet</5>
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| 124 | 124 |
</_join_words> |
| 125 | 125 |
</1> |
| 126 |
<2>$AUTHORITY</2>
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|
| 126 |
<2>$scientificNameAuthorship</2>
|
|
| 127 | 127 |
</_join_words> |
| 128 | 128 |
</value> |
| 129 | 129 |
</_merge_prefix> |
| 130 | 130 |
</taxonomicname> |
| 131 | 131 |
</taxonlabel> |
| 132 | 132 |
</taxonlabel_id> |
| 133 |
<author>$AUTHORITY</author>
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|
| 134 |
<family>$FAMILY</family>
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|
| 135 |
<genus>$GENUS</genus>
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|
| 136 |
<specific_epithet>$SPECIES</specific_epithet>
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|
| 133 |
<author>$scientificNameAuthorship</author>
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| 134 |
<family>$family</family>
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|
| 135 |
<genus>$genus</genus>
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|
| 136 |
<specific_epithet>$specificEpithet</specific_epithet>
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|
| 137 | 137 |
</taxonverbatim> |
| 138 | 138 |
</taxonverbatim_id> |
| 139 | 139 |
</taxondetermination> |
| ... | ... | |
| 141 | 141 |
</locationevent> |
| 142 | 142 |
<locationnarrative> |
| 143 | 143 |
<_merge> |
| 144 |
<1>$LOCATION</1>
|
|
| 144 |
<1>$locality</1>
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|
| 145 | 145 |
<3> |
| 146 | 146 |
<_label> |
| 147 | 147 |
<label>habitat</label> |
| 148 |
<value>$ECOLOGICAL INFORMATION</value>
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|
| 148 |
<value>$habitat</value>
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|
| 149 | 149 |
</_label> |
| 150 | 150 |
</3> |
| 151 | 151 |
</_merge> |
| ... | ... | |
| 157 | 157 |
<coordinates> |
| 158 | 158 |
<latitude_deg> |
| 159 | 159 |
<_dms_to_dd> |
| 160 |
<deg>$LAT DEGREES</deg>
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|
| 161 |
<min>$LAT MINUTES</min>
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| 162 |
<sec>$LAT SECONDS</sec>
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|
| 160 |
<deg>$latitude_deg</deg>
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| 161 |
<min>$latitude_min</min>
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| 162 |
<sec>$latitude_sec</sec>
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| 163 | 163 |
</_dms_to_dd> |
| 164 | 164 |
</latitude_deg> |
| 165 | 165 |
<longitude_deg> |
| 166 | 166 |
<_dms_to_dd> |
| 167 |
<deg>$LONG DEGREES</deg>
|
|
| 168 |
<min>$LONG MINUTES</min>
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|
| 169 |
<sec>$LONG SECONDS</sec>
|
|
| 167 |
<deg>$longitude_deg</deg>
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|
| 168 |
<min>$longitude_min</min>
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| 169 |
<sec>$longitude_sec</sec>
|
|
| 170 | 170 |
</_dms_to_dd> |
| 171 | 171 |
</longitude_deg> |
| 172 | 172 |
</coordinates> |
| 173 | 173 |
</coordinates_id> |
| 174 |
<county>$COUNTY</county>
|
|
| 174 |
<county>$county</county>
|
|
| 175 | 175 |
<matched_place_id> |
| 176 | 176 |
<place> |
| 177 | 177 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
| ... | ... | |
| 180 | 180 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
| 181 | 181 |
<latitude_deg> |
| 182 | 182 |
<_dms_to_dd> |
| 183 |
<deg>$LAT DEGREES</deg>
|
|
| 184 |
<min>$LAT MINUTES</min>
|
|
| 185 |
<sec>$LAT SECONDS</sec>
|
|
| 183 |
<deg>$latitude_deg</deg>
|
|
| 184 |
<min>$latitude_min</min>
|
|
| 185 |
<sec>$latitude_sec</sec>
|
|
| 186 | 186 |
</_dms_to_dd> |
| 187 | 187 |
</latitude_deg> |
| 188 | 188 |
<longitude_deg> |
| 189 | 189 |
<_dms_to_dd> |
| 190 |
<deg>$LONG DEGREES</deg>
|
|
| 191 |
<min>$LONG MINUTES</min>
|
|
| 192 |
<sec>$LONG SECONDS</sec>
|
|
| 190 |
<deg>$longitude_deg</deg>
|
|
| 191 |
<min>$longitude_min</min>
|
|
| 192 |
<sec>$longitude_sec</sec>
|
|
| 193 | 193 |
</_dms_to_dd> |
| 194 | 194 |
</longitude_deg> |
| 195 | 195 |
</coordinates> |
| 196 | 196 |
</coordinates_id> |
| 197 |
<county>$COUNTY</county>
|
|
| 198 |
<stateprovince>$STATE</stateprovince>
|
|
| 197 |
<county>$county</county>
|
|
| 198 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 199 | 199 |
</place> |
| 200 | 200 |
</matched_place_id> |
| 201 |
<stateprovince>$STATE</stateprovince>
|
|
| 201 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 202 | 202 |
</place> |
| 203 | 203 |
</place_id> |
| 204 | 204 |
</locationplace> |
| 205 |
<verbatimelevation>$ELEVATION</verbatimelevation>
|
|
| 205 |
<verbatimelevation>$verbatimElevation</verbatimelevation>
|
|
| 206 | 206 |
</location> |
| 207 | 207 |
</path> |
| 208 | 208 |
</_simplifyPath> |
| inputs/TEX/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 |
TEX,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
ACCESSION NO.,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
ACCESSION NO.,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
|
| 4 |
ACCESSION NO.,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
|
| 5 |
HERBARIUM,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1", |
|
| 6 |
ACCESSION NO.,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
|
| 7 |
ELEVATION,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value", |
|
| 8 |
COLLECTOR NUMBER,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 9 |
LOCATION,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 10 |
ECOLOGICAL INFORMATION,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 11 |
dateCollected,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
|
| 12 |
SPECIMEN NOTES,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1, |
|
| 13 |
COLLECTOR NUMBER,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2, |
|
| 14 |
PHENOLOGY,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/reproductivecondition, |
|
| 15 |
ACCESSION NO.,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
|
| 16 |
HERBARIUM,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_alt/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
|
| 17 |
COLLECTOR NUMBER,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else", |
|
| 18 |
ACCESSION NO.,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 19 |
COLLECTOR NUMBER,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
|
| 20 |
COLLECTOR NAME(S),/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
|
| 21 |
COLLECTOR NUMBER,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 22 |
ORIGIN,"/location/locationevent/taxonoccurrence/iscultivated/_alt/2/_map:[cultivated=t,wild=f,*=]/value", |
|
| 23 |
ORIGIN,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
|
| 24 |
DETERMINED BY,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
|
| 25 |
SPECIES,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet", |
|
| 26 |
GENUS,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet", |
|
| 27 |
FAMILY,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet", |
|
| 28 |
INFRA NAME,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet, |
|
| 29 |
FAMILY,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 30 |
GENUS,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value, |
|
| 31 |
SPECIES,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
|
| 32 |
INFRA NAME,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond", |
|
| 33 |
INFRA NAME,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2, |
|
| 34 |
AUTHORITY,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2, |
|
| 35 |
AUTHORITY,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
|
| 36 |
FAMILY,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 37 |
GENUS,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 38 |
SPECIES,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 39 |
ACCESSION NO.,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
|
| 40 |
COLLECTOR NUMBER,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then", |
|
| 41 |
LOCATION,/location/locationnarrative/_merge/1, |
|
| 42 |
ECOLOGICAL INFORMATION,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?" |
|
| 43 |
LAT DEGREES,/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_dms_to_dd/deg, |
|
| 44 |
LAT MINUTES,/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_dms_to_dd/min, |
|
| 45 |
LAT SECONDS,/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_dms_to_dd/sec, |
|
| 46 |
LONG DEGREES,/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_dms_to_dd/deg, |
|
| 47 |
LONG MINUTES,/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_dms_to_dd/min, |
|
| 48 |
LONG SECONDS,/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_dms_to_dd/sec, |
|
| 49 |
COUNTY,/location/locationplace/*_id/place/county, |
|
| 50 |
LAT DEGREES,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_dms_to_dd/deg", |
|
| 51 |
LAT MINUTES,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_dms_to_dd/min", |
|
| 52 |
LAT SECONDS,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_dms_to_dd/sec", |
|
| 53 |
LONG DEGREES,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_dms_to_dd/deg", |
|
| 54 |
LONG MINUTES,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_dms_to_dd/min", |
|
| 55 |
LONG SECONDS,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_dms_to_dd/sec", |
|
| 56 |
COUNTY,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 57 |
STATE,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 58 |
STATE,/location/locationplace/*_id/place/stateprovince, |
|
| 59 |
ELEVATION,/location/verbatimelevation, |
|
| 60 |
COLL. DATE (EXACT),,** No join mapping for dateCollected__scrubbed ** |
|
| 61 |
COLL. DATE (GENERAL),,** No join mapping for dateCollected__verbatim ** |
|
| 62 |
DATA EDITED DATE,,** No join mapping for modified ** |
|
| 63 |
DATA ENTRY BY,,** No join mapping for *DATA ENTRY BY ** |
|
| 64 |
DATA ENTRY DATE,,** No join mapping for *DATA ENTRY DATE ** |
|
| 65 |
DET NOTES,,** No join mapping for identificationRemarks ** |
|
| 66 |
INFRA AUTHORITY,,** No join mapping for *INFRA AUTHORITY ** |
|
| 67 |
INFRA RANK,,** No join mapping for infraspecificRank ** |
|
| 68 |
LAT NS,,** No join mapping for *LAT NS ** |
|
| 69 |
LONG EW,,** No join mapping for *LONG EW ** |
|
| 70 |
SOURCE OF LATLONG,,** No join mapping for *SOURCE OF LATLONG ** |
|
| 71 |
UTM,,** No join mapping for *UTM ** |
|
| 72 |
row_num,,** No join mapping for *row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 73 | 2 | |
| inputs/TEX/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run
|
|
| 0 | 3 | |
| inputs/TEX/Specimen2/postprocess.sql | ||
|---|---|---|
| 2 | 2 |
|
| 3 | 3 |
|
| 4 | 4 |
SELECT mk_derived_col((:table_str, 'dateCollected'), |
| 5 |
$$_alt("EXACT DATE", "GENERAL DATE")$$)
|
|
| 5 |
$$_alt("dateCollected__scrubbed", "dateCollected__verbatim")$$)
|
|
| 6 | 6 |
; -- runtime: 0.3 s ("Time: 283.170 ms") @starscream
|
| 7 | 7 |
|
| 8 | 8 |
|
| 9 | 9 |
SELECT mk_derived_col((:table_str, 'recordedBy__primary'), |
| 10 |
$$_join_words("COLLECTOR 1 FIRST NAME", "COLLECTOR 1 LAST NAME")$$)
|
|
| 10 |
$$_join_words("recordedBy__primary__first", "recordedBy__primary__last")$$)
|
|
| 11 | 11 |
; -- runtime: 0.2 s ("Time: 154.234 ms") @starscream
|
| 12 | 12 |
|
| 13 | 13 |
SELECT mk_derived_col((:table_str, 'recordedBy__additional__1'), |
| 14 |
$$_join_words("COLLECTOR 2 FIRST NAME", "COLLECTOR 2 LAST NAME")$$)
|
|
| 14 |
$$_join_words("recordedBy__additional__1__first", "recordedBy__additional__1__last")$$)
|
|
| 15 | 15 |
; -- runtime: 0.1 s ("Time: 135.107 ms") @starscream
|
| 16 | 16 |
|
| 17 | 17 |
SELECT mk_derived_col((:table_str, 'recordedBy__additional__2'), |
| 18 |
$$_join_words("COLLECTOR 3 FIRST NAME", "COLLECTOR 3 LAST NAME")$$)
|
|
| 18 |
$$_join_words("recordedBy__additional__2__first", "recordedBy__additional__2__last")$$)
|
|
| 19 | 19 |
; -- runtime: 0.1 s ("Time: 133.670 ms") @starscream
|
| 20 | 20 |
|
| 21 | 21 |
SELECT mk_derived_col((:table_str, 'recordedBy__additional__3'), |
| 22 |
$$_join_words("COLLECTOR 4 FIRST NAME", "COLLECTOR 4 LAST NAME")$$)
|
|
| 22 |
$$_join_words("recordedBy__additional__3__first", "recordedBy__additional__3__last")$$)
|
|
| 23 | 23 |
; -- runtime: 0.1 s ("Time: 132.596 ms") @starscream
|
| 24 | 24 |
|
| 25 | 25 |
SELECT mk_derived_col((:table_str, 'recordedBy__additional__4'), |
| 26 |
$$_join_words("COLLECTOR 5 FIRST NAME", "COLLECTOR 5 LAST NAME")$$)
|
|
| 26 |
$$_join_words("recordedBy__additional__4__first", "recordedBy__additional__4__last")$$)
|
|
| 27 | 27 |
; -- runtime: 0.1 s ("Time: 132.078 ms") @starscream
|
| 28 | 28 |
|
| 29 | 29 |
SELECT mk_derived_col((:table_str, 'recordedBy'), |
| ... | ... | |
| 32 | 32 |
|
| 33 | 33 |
|
| 34 | 34 |
SELECT mk_derived_col((:table_str, 'identifiedBy'), |
| 35 |
$$_join_words("DETERMINER FIRST NAME", "DETERMINER LAST NAME")$$)
|
|
| 35 |
$$_join_words("identifiedBy__first", "identifiedBy__last")$$)
|
|
| 36 | 36 |
; -- runtime: 0.3 s ("Time: 267.310 ms") @starscream
|
| inputs/TEX/Specimen2/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/TEX/Specimen2/map.csv | ||
|---|---|---|
| 44 | 44 |
DET DATE,dateIdentified,, |
| 45 | 45 |
DETERMINER INSTITUTION,*DETERMINER INSTITUTION,, |
| 46 | 46 |
DET NOTES,identificationRemarks,, |
| 47 |
dateCollected,dateCollected,, |
|
| 48 |
recordedBy__primary,recordedBy__primary,, |
|
| 49 |
recordedBy__additional__1,recordedBy__additional__1,, |
|
| 50 |
recordedBy__additional__2,recordedBy__additional__2,, |
|
| 51 |
recordedBy__additional__3,recordedBy__additional__3,, |
|
| 52 |
recordedBy__additional__4,recordedBy__additional__4,, |
|
| 53 |
recordedBy,recordedBy,, |
|
| 54 |
identifiedBy,identifiedBy,, |
|
| inputs/TEX/Specimen2/test.xml.ref | ||
|---|---|---|
| 11 | 11 |
<_units> |
| 12 | 12 |
<to>m</to> |
| 13 | 13 |
<to></to> |
| 14 |
<value>$ELEVATION</value>
|
|
| 14 |
<value>$verbatimElevation</value>
|
|
| 15 | 15 |
</_units> |
| 16 | 16 |
</elevation_m> |
| 17 | 17 |
<iscultivated> |
| 18 | 18 |
<_locationnarrative_is_cultivated> |
| 19 | 19 |
<locationnarrative> |
| 20 | 20 |
<_join> |
| 21 |
<1>$LOCALITY</1>
|
|
| 22 |
<3>$VEGETATION</3>
|
|
| 21 |
<1>$locality</1>
|
|
| 22 |
<3>$habitat</3>
|
|
| 23 | 23 |
</_join> |
| 24 | 24 |
</locationnarrative> |
| 25 | 25 |
</_locationnarrative_is_cultivated> |
| ... | ... | |
| 28 | 28 |
<taxonoccurrence> |
| 29 | 29 |
<aggregateoccurrence> |
| 30 | 30 |
<collectiondate>$dateCollected</collectiondate> |
| 31 |
<notes>$PLANT DATA</notes>
|
|
| 31 |
<notes>$occurrenceRemarks</notes>
|
|
| 32 | 32 |
<plantobservation> |
| 33 |
<authorplantcode>$COLLECTOR NUMBER</authorplantcode>
|
|
| 34 |
<reproductivecondition>$PHENOLOGY</reproductivecondition>
|
|
| 33 |
<authorplantcode>$collectorNumber</authorplantcode>
|
|
| 34 |
<reproductivecondition>$reproductiveCondition</reproductivecondition>
|
|
| 35 | 35 |
<specimenreplicate> |
| 36 |
<collectioncode_dwc>$HERBARIUM</collectioncode_dwc>
|
|
| 37 |
<collectionnumber>$COLLECTOR NUMBER</collectionnumber>
|
|
| 36 |
<collectioncode_dwc>$collection</collectioncode_dwc>
|
|
| 37 |
<collectionnumber>$collectorNumber</collectionnumber>
|
|
| 38 | 38 |
</specimenreplicate> |
| 39 | 39 |
</plantobservation> |
| 40 | 40 |
</aggregateoccurrence> |
| ... | ... | |
| 44 | 44 |
<cultivated>t</cultivated> |
| 45 | 45 |
<wild>f</wild> |
| 46 | 46 |
<*></*> |
| 47 |
<value>$ORIGIN</value>
|
|
| 47 |
<value>$establishmentMeans</value>
|
|
| 48 | 48 |
</_map> |
| 49 | 49 |
</iscultivated> |
| 50 | 50 |
<isnative> |
| ... | ... | |
| 52 | 52 |
<native>t</native> |
| 53 | 53 |
<exotic>f</exotic> |
| 54 | 54 |
<*></*> |
| 55 |
<value>$ORIGIN</value>
|
|
| 55 |
<value>$establishmentMeans</value>
|
|
| 56 | 56 |
</_map> |
| 57 | 57 |
</isnative> |
| 58 | 58 |
<taxondetermination> |
| ... | ... | |
| 72 | 72 |
<parent_id> |
| 73 | 73 |
<taxonlabel> |
| 74 | 74 |
<rank>variety</rank> |
| 75 |
<taxonepithet>$VARIETY</taxonepithet>
|
|
| 75 |
<taxonepithet>$variety</taxonepithet>
|
|
| 76 | 76 |
<parent_id> |
| 77 | 77 |
<taxonlabel> |
| 78 | 78 |
<rank>subspecies</rank> |
| 79 |
<taxonepithet>$SUBSPECIES</taxonepithet>
|
|
| 79 |
<taxonepithet>$subspecies</taxonepithet>
|
|
| 80 | 80 |
<parent_id> |
| 81 | 81 |
<taxonlabel> |
| 82 | 82 |
<rank>species</rank> |
| 83 |
<taxonepithet>$SPECIES</taxonepithet>
|
|
| 83 |
<taxonepithet>$specificEpithet</taxonepithet>
|
|
| 84 | 84 |
<parent_id> |
| 85 | 85 |
<taxonlabel> |
| 86 | 86 |
<rank>genus</rank> |
| 87 |
<taxonepithet>$GENUS</taxonepithet>
|
|
| 87 |
<taxonepithet>$genus</taxonepithet>
|
|
| 88 | 88 |
<parent_id> |
| 89 | 89 |
<taxonlabel> |
| 90 | 90 |
<rank>family</rank> |
| 91 |
<taxonepithet>$FAMILY</taxonepithet>
|
|
| 91 |
<taxonepithet>$family</taxonepithet>
|
|
| 92 | 92 |
</taxonlabel> |
| 93 | 93 |
</parent_id> |
| 94 | 94 |
</taxonlabel> |
| ... | ... | |
| 107 | 107 |
</parent_id> |
| 108 | 108 |
<taxonomicname> |
| 109 | 109 |
<_merge_prefix> |
| 110 |
<prefix><_taxon_family_require_std><family>$FAMILY</family></_taxon_family_require_std></prefix>
|
|
| 110 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
|
|
| 111 | 111 |
<value> |
| 112 | 112 |
<_join_words> |
| 113 | 113 |
<1> |
| 114 | 114 |
<_join_words> |
| 115 |
<2><_filter_genus><value>$GENUS</value></_filter_genus></2>
|
|
| 116 |
<3>$SPECIES</3>
|
|
| 117 |
<4>$SUBSPECIES</4>
|
|
| 115 |
<2><_filter_genus><value>$genus</value></_filter_genus></2>
|
|
| 116 |
<3>$specificEpithet</3>
|
|
| 117 |
<4>$subspecies</4>
|
|
| 118 | 118 |
<6> |
| 119 | 119 |
<_join_words> |
| 120 | 120 |
<1>var. </1> |
| 121 |
<2>$VARIETY</2>
|
|
| 121 |
<2>$variety</2>
|
|
| 122 | 122 |
</_join_words> |
| 123 | 123 |
</6> |
| 124 | 124 |
</_join_words> |
| 125 | 125 |
</1> |
| 126 |
<2>$SPECIES AUTHORITY</2>
|
|
| 126 |
<2>$scientificNameAuthorship</2>
|
|
| 127 | 127 |
</_join_words> |
| 128 | 128 |
</value> |
| 129 | 129 |
</_merge_prefix> |
| 130 | 130 |
</taxonomicname> |
| 131 | 131 |
</taxonlabel> |
| 132 | 132 |
</taxonlabel_id> |
| 133 |
<author>$SPECIES AUTHORITY</author>
|
|
| 134 |
<family>$FAMILY</family>
|
|
| 135 |
<genus>$GENUS</genus>
|
|
| 136 |
<specific_epithet>$SPECIES</specific_epithet>
|
|
| 133 |
<author>$scientificNameAuthorship</author>
|
|
| 134 |
<family>$family</family>
|
|
| 135 |
<genus>$genus</genus>
|
|
| 136 |
<specific_epithet>$specificEpithet</specific_epithet>
|
|
| 137 | 137 |
</taxonverbatim> |
| 138 | 138 |
</taxonverbatim_id> |
| 139 |
<determinationdate><_dateRangeStart><value>$DET DATE</value></_dateRangeStart></determinationdate>
|
|
| 139 |
<determinationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></determinationdate>
|
|
| 140 | 140 |
</taxondetermination> |
| 141 | 141 |
</taxonoccurrence> |
| 142 | 142 |
</locationevent> |
| 143 | 143 |
<locationnarrative> |
| 144 | 144 |
<_merge> |
| 145 |
<1>$LOCALITY</1>
|
|
| 145 |
<1>$locality</1>
|
|
| 146 | 146 |
<3> |
| 147 | 147 |
<_label> |
| 148 | 148 |
<label>habitat</label> |
| 149 |
<value>$VEGETATION</value>
|
|
| 149 |
<value>$habitat</value>
|
|
| 150 | 150 |
</_label> |
| 151 | 151 |
</3> |
| 152 |
<4>$MISC NOTES</4>
|
|
| 152 |
<4>$locationRemarks</4>
|
|
| 153 | 153 |
</_merge> |
| 154 | 154 |
</locationnarrative> |
| 155 | 155 |
<locationplace> |
| ... | ... | |
| 157 | 157 |
<place> |
| 158 | 158 |
<coordinates_id> |
| 159 | 159 |
<coordinates> |
| 160 |
<latitude_deg><_dms_to_dd><value>$LATITUDE</value></_dms_to_dd></latitude_deg>
|
|
| 161 |
<longitude_deg><_dms_to_dd><value>$LONGITUDE</value></_dms_to_dd></longitude_deg>
|
|
| 162 |
<verbatimlatitude>$LATITUDE</verbatimlatitude>
|
|
| 163 |
<verbatimlongitude>$LONGITUDE</verbatimlongitude>
|
|
| 160 |
<latitude_deg><_dms_to_dd><value>$latitude_DMS</value></_dms_to_dd></latitude_deg>
|
|
| 161 |
<longitude_deg><_dms_to_dd><value>$longitude_DMS</value></_dms_to_dd></longitude_deg>
|
|
| 162 |
<verbatimlatitude>$latitude_DMS</verbatimlatitude>
|
|
| 163 |
<verbatimlongitude>$longitude_DMS</verbatimlongitude>
|
|
| 164 | 164 |
</coordinates> |
| 165 | 165 |
</coordinates_id> |
| 166 |
<county>$COUNTY</county>
|
|
| 166 |
<county>$county</county>
|
|
| 167 | 167 |
<matched_place_id> |
| 168 | 168 |
<place> |
| 169 | 169 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
| 170 | 170 |
<coordinates_id> |
| 171 | 171 |
<coordinates> |
| 172 | 172 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
| 173 |
<latitude_deg><_dms_to_dd><value>$LATITUDE</value></_dms_to_dd></latitude_deg>
|
|
| 174 |
<longitude_deg><_dms_to_dd><value>$LONGITUDE</value></_dms_to_dd></longitude_deg>
|
|
| 173 |
<latitude_deg><_dms_to_dd><value>$latitude_DMS</value></_dms_to_dd></latitude_deg>
|
|
| 174 |
<longitude_deg><_dms_to_dd><value>$longitude_DMS</value></_dms_to_dd></longitude_deg>
|
|
| 175 | 175 |
</coordinates> |
| 176 | 176 |
</coordinates_id> |
| 177 |
<county>$COUNTY</county>
|
|
| 178 |
<stateprovince>$STATE</stateprovince>
|
|
| 177 |
<county>$county</county>
|
|
| 178 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 179 | 179 |
</place> |
| 180 | 180 |
</matched_place_id> |
| 181 |
<stateprovince>$STATE</stateprovince>
|
|
| 181 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 182 | 182 |
</place> |
| 183 | 183 |
</place_id> |
| 184 | 184 |
</locationplace> |
| 185 |
<verbatimelevation>$ELEVATION</verbatimelevation>
|
|
| 185 |
<verbatimelevation>$verbatimElevation</verbatimelevation>
|
|
| 186 | 186 |
</location> |
| 187 | 187 |
</path> |
| 188 | 188 |
</_simplifyPath> |
| inputs/TEX/Specimen2/VegBIEN.csv | ||
|---|---|---|
| 1 |
TEX,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
HERBARIUM,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1", |
|
| 3 |
ELEVATION,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value", |
|
| 4 |
COLLECTOR NUMBER,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 5 |
LOCALITY,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 6 |
VEGETATION,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
|
| 7 |
DET DATE,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/1/_dateRangeStart/value", |
|
| 8 |
dateCollected,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
|
| 9 |
PLANT DATA,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1, = specimenDescription |
|
| 10 |
COLLECTOR NUMBER,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2, |
|
| 11 |
PHENOLOGY,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/reproductivecondition, |
|
| 12 |
HERBARIUM,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_alt/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
|
| 13 |
COLLECTOR NUMBER,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else", |
|
| 14 |
COLLECTOR NUMBER,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
|
| 15 |
recordedBy,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
|
| 16 |
COLLECTOR NUMBER,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 17 |
ORIGIN,"/location/locationevent/taxonoccurrence/iscultivated/_alt/2/_map:[cultivated=t,wild=f,*=]/value", |
|
| 18 |
ORIGIN,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
|
| 19 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
|
| 20 |
VARIETY,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=variety]/taxonepithet", |
|
| 21 |
SUBSPECIES,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=subspecies]/taxonepithet", |
|
| 22 |
SPECIES,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet", |
|
| 23 |
GENUS,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet", |
|
| 24 |
FAMILY,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet", |
|
| 25 |
FAMILY,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 26 |
GENUS,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value, |
|
| 27 |
SPECIES,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
|
| 28 |
SUBSPECIES,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4, |
|
| 29 |
VARIETY,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/6/_join_words:[1=""var. ""]/2", |
|
| 30 |
SPECIES AUTHORITY,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2, |
|
| 31 |
SPECIES AUTHORITY,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author, |
|
| 32 |
FAMILY,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 33 |
GENUS,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
|
| 34 |
SPECIES,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
|
| 35 |
DET DATE,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value, |
|
| 36 |
COLLECTOR NUMBER,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then", |
|
| 37 |
LOCALITY,/location/locationnarrative/_merge/1, |
|
| 38 |
VEGETATION,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?" |
|
| 39 |
MISC NOTES,/location/locationnarrative/_merge/4, |
|
| 40 |
LATITUDE,/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_dms_to_dd/value, |
|
| 41 |
LONGITUDE,/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_dms_to_dd/value, |
|
| 42 |
LATITUDE,/location/locationplace/*_id/place/*_id/coordinates/verbatimlatitude, |
|
| 43 |
LONGITUDE,/location/locationplace/*_id/place/*_id/coordinates/verbatimlongitude, |
|
| 44 |
COUNTY,/location/locationplace/*_id/place/county, |
|
| 45 |
LATITUDE,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_dms_to_dd/value", |
|
| 46 |
LONGITUDE,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_dms_to_dd/value", |
|
| 47 |
COUNTY,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 48 |
STATE,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 49 |
STATE,/location/locationplace/*_id/place/stateprovince, |
|
| 50 |
ELEVATION,/location/verbatimelevation, |
|
| 51 |
BARCODE,,** No join mapping for barcode ** |
|
| 52 |
COLLECTOR 1 FIRST NAME,,** No join mapping for recordedBy__primary__first ** |
|
| 53 |
COLLECTOR 1 LAST NAME,,** No join mapping for recordedBy__primary__last ** |
|
| 54 |
COLLECTOR 2 FIRST NAME,,** No join mapping for recordedBy__additional__1__first ** |
|
| 55 |
COLLECTOR 2 LAST NAME,,** No join mapping for recordedBy__additional__1__last ** |
|
| 56 |
COLLECTOR 3 FIRST NAME,,** No join mapping for recordedBy__additional__2__first ** |
|
| 57 |
COLLECTOR 3 LAST NAME,,** No join mapping for recordedBy__additional__2__last ** |
|
| 58 |
COLLECTOR 4 FIRST NAME,,** No join mapping for recordedBy__additional__3__first ** |
|
| 59 |
COLLECTOR 4 LAST NAME,,** No join mapping for recordedBy__additional__3__last ** |
|
| 60 |
COLLECTOR 5 FIRST NAME,,** No join mapping for recordedBy__additional__4__first ** |
|
| 61 |
COLLECTOR 5 LAST NAME,,** No join mapping for recordedBy__additional__4__last ** |
|
| 62 |
DATABASED BY,,** No join mapping for *DATABASED BY ** |
|
| 63 |
DET NOTES,,** No join mapping for identificationRemarks ** |
|
| 64 |
DETERMINER FIRST NAME,,** No join mapping for identifiedBy__first ** |
|
| 65 |
DETERMINER INSTITUTION,,** No join mapping for *DETERMINER INSTITUTION ** |
|
| 66 |
DETERMINER LAST NAME,,** No join mapping for identifiedBy__last ** |
|
| 67 |
END DATE,,** No non-empty join mapping for UNUSED#END DATE ** |
|
| 68 |
EXACT DATE,,** No join mapping for dateCollected__scrubbed ** |
|
| 69 |
GENERAL DATE,,** No join mapping for dateCollected__verbatim ** |
|
| 70 |
LATLONG DATUM,,** No join mapping for *LATLONG DATUM ** |
|
| 71 |
LATLONG SOURCE,,** No join mapping for *LATLONG SOURCE ** |
|
| 72 |
SUBSPECIES AUTHOR,,** No join mapping for *SUBSPECIES AUTHOR ** |
|
| 73 |
UTM,,** No join mapping for *UTM ** |
|
| 74 |
VARIETY AUTHOR,,** No join mapping for *VARIETY AUTHOR ** |
|
| 75 |
recordedBy__additional__1,,** No join mapping for recordedBy__additional__1 ** |
|
| 76 |
recordedBy__additional__2,,** No join mapping for recordedBy__additional__2 ** |
|
| 77 |
recordedBy__additional__3,,** No join mapping for recordedBy__additional__3 ** |
|
| 78 |
recordedBy__additional__4,,** No join mapping for recordedBy__additional__4 ** |
|
| 79 |
recordedBy__primary,,** No join mapping for recordedBy__primary ** |
|
| 80 |
row_num,,** No join mapping for *row_num ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 81 | 2 | |
| inputs/TEX/Specimen2/unmapped_terms.csv | ||
|---|---|---|
| 22 | 22 |
identifiedBy__last |
| 23 | 23 |
*DETERMINER INSTITUTION |
| 24 | 24 |
identificationRemarks |
| 25 |
recordedBy__primary |
|
| 26 |
recordedBy__additional__1 |
|
| 27 |
recordedBy__additional__2 |
|
| 28 |
recordedBy__additional__3 |
|
| 29 |
recordedBy__additional__4 |
|
Also available in: Unified diff
inputs/TEX/: switched to new-style import, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource